Unfortunately, no. VoiceThread just creates one course for all of your course’s sections and enrolls students from all of them in it. However, there is an option for a workaround: manually creating a group for each section.
Manually creating groups for your sections in VoiceThread
Students in a combined-section Canvas course won’t really have any issues if you’re just creating lecture presentations or “Watch” assignments with VoiceThread.
However, if you plan to use VoiceThread for “Create” or “Comment” assignments, students will be able to see one another’s presentations and/or comments across all of your sections, so you’ll want to manually create groups in VoiceThread for each section. Fortunately, the students in all of your sections will appear in your VoiceThread account since it’ll recognize them through your combined-section Canvas course’s enrollment.
The challenge, here, is with sharing. You and your students will need to make sure you’re sharing your VoiceThread presentations with their section’s group rather than the VoiceThread class.